During a scary thunderstorm, Pajama Sam journeys through his attic and up into the clouds to World Wide Weather. While confronting a surprisingly kind Thunder and Lightning, Sam accidentally causes a major malfunction and so is tasked with retrieving several missing important parts, before the CEO and president of WWW, Mother Nature, (an onion,) finds out. The side objective of this game is to find all of the missing puzzle pieces, which will form an amusing picture when they are all collected.